The Appearance of the Apprentice
by meggynicaoidh
Summary: What happens when a serial killer with an extremely familiar MO reemerges and targets the team? Case AU. This is set about 2 years in the future. Rated T for language.
1. Chapter 1

_**A/N: I've been inspired by all of the case fics recently so I decided to take a stab at writing my own. I hope you enjoy it!**_

* * *

The harsh sunlight burned into Booth's retinas as he walked alongside his wife to the crime scene. The victim had been found by a jogger at 7am and had been dumped in the middle of the park, exposed. As they crossed the yellow tape and politely greeted the FBI techs, Booth privately wished the sunlight had succeeded in blinding him. The victim laid splayed on the grass, in the later stages of decomposition, with their skull badly damaged. Booth averted his gaze from the body and greeted Cam, who was retrieving evidence bags from the Jeffersonian van.

Brennan crouched down next to the victim and addressed her intern. "What have you determined so far, Dr. Bray?"

"The victim is a female. The wear on her incisors suggests she is in her early thirties. Furthermore, the angle of her pelvis suggests she has given birth before. Lacerations to her carpal bones also suggest that she was bound by her killer."

"I concur, very good Dr. Bray." Wendell smiled slightly and caught Hodgins' eye, who was examining the insects found on the body.

"These blow fly larvae suggest that the victim has been dead for 5 to 6 days. Any sign of cause of death?"

Brennan sighed. "No. Her skull is very badly damaged, meaning a facial reconstruction will be very challenging. I imagine the killer wanted to obscure the victim's identity."

"Oh no!" Hodgins exclaimed in horror.

"What is it, Hodgins?" Booth queried.

He inhaled sharply and slowly raised his hand from the victim's maggot filled oesophagus, a small object held between his tweezers. Everyone exchanged looks of worry and fear.

"Shit." Booth mumbled. "What does it mean, Hodgins?"

Hodgins swallowed. "Uh… It's a black begonia. It means beware." Hodgins examined the flower more closely and discovered something. "Hey you guys, this was hidden within the petals."

He handed a platinum wedding ring over to Booth, who held it with an evidence bag. "Hey, there's an inscription on the inside. The 31st of August 2016."

"Perhaps this will help us determine the victim's identity." Brennan said hopefully. "Dr Saroyan, is Dr. Vaziri scheduled to work today?"

"Uh no, Arastoo is giving a lecture at the University of Virginia on how to determine the signs of abuse on a badly degraded set of remains. But I can call him and ask him to come to the lab when he's finished."

"Thank you, that would be helpful. I feel that we are going to need as much help as possible on this case."

"I'll call Daisy." Booth offered. "She can drop Lance off at ours, Max won't mind." Brennan and Cam nodded in agreement.

Cam cleared her throat and began to rise. "Well, I'll get the techs to prep the body for the lab. Dr. Hodgins, can you please call Dr. Wells to assist with gathering particulate evidence?"

Before everyone had a chance to protest, Cam interjected. "Yes, I know. Dr. Wells is a pain in the ass but he is genius. He also happens to be the only intern qualified to assist Dr. Hodgins in cataloguing such evidence which may prove vital to solving the case."

Everyone sighed and gazed at the body, knowing that Cam was right.

* * *

As Booth drove himself and Brennan back to the lab, he glanced sideways at his wife and noticed her jaw was clenched.

"You okay, Bones?"

"I'm fine." She lied.

"Come on, Bones, you know I know you better than that. What's wrong?"

"I just-" she began and sighed, her voice becoming emotional. "I know it's impossible but-"

"You think Pelant is back. Bones, he's dead. I shot him, you examined his body yourself and Cam signed off his autopsy and we watched him be cremated. There's no way this is him."

"I know that, Booth. I just can't help thinking of the terrible things he put us through. And our friends." She blinked back tears, feeling guilty. "Booth, there is something I need to tell you. I now realise I should have told you this a long time ago. But it was at a point in our lives where telling you wouldn't have mattered because we would no longer be associated with such a person."

"What are you talking about, Bones?" he asked, shifting uncomfortably in his seat.

"At the end of our last case before our retirement 2 years ago, Angela was able to fully reconstruct the data on Cooper's microchip. She found a video she thought I should see. It was Pelant. He said that if we were watching the video it meant that he was dead, but he warned that his legacy would continue. Perhaps this killer intends to carry on Pelant's legacy."

Booth sat in stunned silence, focusing hard on the road in front of him. He couldn't believe this. How could she have kept this from him? After everything that they had been through, did he not deserve to know?

"Jesus, Bones! Were you ever planning on telling me this?" He asked, clearly annoyed.

"I had thought about it several times, but there never seemed to be an appropriate moment. We were leaving this life behind so I didn't see fit to worry you with it when it would be completely out with our control, especially when nothing ever amounted from it… Until now at least. I had hoped it was just an empty threat."

"Well it clearly wasn't, was it?" he tightened his grip on the steering wheel and avoided her gaze.

"I don't want to fight with you, Booth. That's probably what the killer wants. We should just focus on the case and not worry about the details."

He relaxed his grip. "You're right. We're going to need that ID asap. Knowing who the victim is might help us gauge who the killer could be. I'll head back to the Hoover and look over Pelant's files. God, I wish Aubrey was here. He told me he had gone through the files with Sweets while I was in prison, so he might even remember some of Sweets' insights." He sighed deeply. "But I can't interrupt his honeymoon when we don't even have anything to go on."

"I know how you feel. Dr. Warren is the best out of my interns at reassembling the skull, as well as the entire skeleton. Her expertise would be invaluable to this case." She admitted.

* * *

Brennan swiped herself onto the platform and was greeted by Wendell, Clark and Daisy. "What have you all determined so far?"

Daisy perked up. "The victim's teeth were almost entirely destroyed barre three but luckily for us she had a rather misshapen third molar."

"I dissected the other third molar, it appears the victim was born and raised in central Los Angeles. We've sent the data to Angela to see if she can find an ID based on the victim's height, weight and marital status."

Just as Arastoo had finished speaking, Angela swiped herself onto the platform, a slightly distressed look on her face.

"Angie? What is it?" Hodgins asked.

"It's Genny." She said emotionally. "It's Agent Shaw."

The platform fell silent. Agent Shaw had assisted on many cases throughout the past 8 years, the most notable of which was the capture of Jacob Broadsky. Her determination made her an excellent agent but over the years she would join the team after a case for dinner or some drinks, and they had come to consider her a close friend.

"Oh." Brennan said sadly, breaking the silence. "Booth will be very upset to hear this."

"The bastard." Hodgins said angrily. "He's targeting us, just like Pelant did."

Before anyone had a chance to respond to Hodgins' remarks the Jeffersonian lost all power. There were then two loud thumps on the platform behind them. No one had time to react before both canisters rapidly emitted strong gas, leaving everyone unconscious… exposed.

Oooooooooooo

Booth pinched the bridge of his nose as he sat slumped over Pelant's thick files. He wiped his face with the back of his hand as he rose to get his seventh coffee of the day. He stopped short when his phone rang.

"Booth." he answered automatically.

"Seeley! Oh my god Seeley-"

"Cam?" He was about to object to the use of his first name but thought better of it when he heard the distress in her voice. "What's the matter?"

"I just got back from the crime scene and I was about to tell Dr. Hodgins to go back and meet Dr. Wells to finish gathering trace when I found the lab in total darkness." She began to cry. "Everyone on the platform was knocked unconscious by an unknown substance, and they're being attended to by medics just now. But, Booth…" She inhaled slowly. "Dr. Brennan isn't here. She's gone."

 **Review? :) I'd love to hear what you think, and if you want me to continue with the story.**


	2. Chapter 2

**A/N: Sorry for the delay in getting this chapter out, I've been working a lot and not really feeling 100%, but I hope you enjoy it!**

* * *

Booth hung up the phone and threw it forcefully at the wall. His heart thumped so loud he didn't even hear the sound of his cell smashing into a hundred pieces. He began to shake uncontrollably. What was he going to tell Christine? And Hank? And Max? It was approaching lunch time and he knew he'd have to call Hank soon to make sure he was OK. He still cried every morning when they both went to work. He loved Max but he was still very attached to his parents.

Booth sighed audibly and let out a small cry. It was Bones' turn to call him. He would be upset when Booth called and not his mom, but trying to explain the situation to him would be futile because he was too young to understand. He decided to avoid the call altogether, deciding instead that he would go home at 2pm and tell Max and the kids in person. He checked his watch. That gave him almost three hours to come up with a plan of how to tell them. And to find his wife. He snatched his jacket from the back of his chair and headed towards the parking garage, determined to find out what the hell happened at the Jeffersonian.

* * *

As Brennan's eyes opened and adjusted to the dim light, she began to panic. Her mouth was gagged. Her hands and feet tied. Her eyes felt very dry. She searched the room for any other sign of life but soon realised she was alone. She quickly rolled onto her back and used her fingers to help raise her into a sitting position, biting her lip as she thought of an escape plan. She sat in concentrated silence for a few minutes, calculations whirring through her mind. She then sighed, defeated.

"The probability of escaping unassisted while immobilised is zero." She huffed. She began to scoot around the large room on her bottom, stopping after a few moments as a memory flooded into her mind. She recalled a night in the Mighty Hut when Christine was still very young and learning to walk. Although she was very advanced for her age, she was always too afraid to walk down the stairs by herself, no matter how many times Booth and Brennan illustrated how easy it was. Eventually Booth relented and grabbed a pillow from the master bedroom, placing himself on top of it and fixing Christine to his lap. Brennan recalled being momentarily confused at the sight, until the two of them came skidding down the stairs, roaring with laughter. She was about to lecture Booth about the dangers of the activity but found that she couldn't concentrate on anything other than the sound of their laughter. She had never heard Christine laugh so hard, and Brennan longed to be involved in their fun. For the rest of that night the three of them slid down the staircase into a gigantic pile of blankets and sofa cushions, laughing until their sides ached.

As the sound of their laughter echoed in her ears, Brennan wiped away the hot tears that had gathered at the base of her chin onto her blouse. She sighed as she blinked back more tears and tried to calm her breathing.

"I'm being foolish. Booth will find me." She thought decisively.

* * *

Having determined nothing of use from his conversations with Hodgins, Angela, Daisy, Wendell or Clark, Booth admitted the only thing left to do was to return home and tell Max what had happened.

As he reached for the door knob he let out a deep sigh and shook his head slightly. After several moments of debating whether to go inside or get back in his car and drive away, he twisted the handle, revealing a couple of excited children coming towards him.

"Daddy!" they both yelled before launching themselves into his arms.

He feigned enthusiasm, earning him a concerned look from Max. "Hey! How are my monkeys doing today?"

Before Christine could answer, Max interrupted. "Hey Christine, why don't you guys head down to your room and stick one of those nice movies on so I can talk to your dad."

"Ok Grandpa!"

They both stared at the children as they skipped down the hall together, oblivious to the danger their mother was in. Booth sighed audibly.

"Alright Booth, what the hell is going on? Since when aren't you excited to see your kids?"

Booth's eyes dropped to the floor. He felt ashamed to tell Max. He felt like it was his fault. He was supposed to protect her and he'd let her down.

"Bones… she's gone. She's been kidnapped, Max."

"What?! When? By who?"

"About 5 hours ago. And we don't know yet, but we have a pretty good idea. Listen Max, this guy… he's dangerous. Very dangerous-"

"What, like, Pelant dangerous?"

Booth raised his eyes and stared intently at his father-in-law. "Pelant dangerous." He confirmed.

Max wiped his face in frustration. He couldn't stand his family being in dangerous situations like this. He also couldn't stand that Booth wouldn't just let him kill these people. He didn't care about going to jail as long as there were all safe.

Booth cut into Max's train of thoughts. "Listen, I need you and the kids to go. I need you to get as far away as possible. Hell, why don't you go stay with Russ, Amy and the girls? They haven't seen Hank since he was born. Just get the hell out of D.C."

Max nodded and immediately left for his room to pack a bag. Booth watched him go as he listened to his kids' laughter coming from Christine's bedroom. The sound made his stomach drop. How long would it be before he would hear that sound again? When he next heard it, would Bones be there to hear it too?

He heard Max shuffling around Christine's room, packing a bag for the children and cutting their movie off. They began to protest when Max announced that they were going to visit Russ and Amy.

"Yay! Uncle Russ!" they both yelled as Max shoved them down the hallway to the front door.

They stopped to say goodbye to Booth, who had a lump so big in his throat that he was certain he'd choke any second. "Goodbye baby, I'll see you soon. Tell Russ and the girls that Mommy and I say hello."

Christine giggled before leaning in for a kiss and cuddle. "I will, Daddy. Love you."

"I love you too." he said fighting back tears, not wanting to scare her. She may only be eight years old, but she's not stupid. As she turned to go outside to the car, Hank's chubby frame came stomping over to Booth.

"Bye, Dada! Wub you." he said as his chubby hands played with Booth's cheeks.

"Goodbye, Buddy. I love you too." Booth pressed his small frame against his, never wanting to let go, but knowing it was for the best.

Max lifted Hank, put him beside Christine by the front door and told them to wait by the car. He turned 180 degrees to face Booth. He walked over to him and placed his hand on Booth's right shoulder. "Get her back, Booth. If anyone can do it, it's you. I trust you. I'll take good care of them and I'll call you when we reach Atlanta."

With that, Max left swiftly, and the last sound Booth heard was Max's car screeching out of the driveway. Booth plodded over to the breakfast bar, sat down and began to cry.

He wasn't sure how long he'd been sitting there for. It felt like forever. He continued to sob, his ears ringing. His own voice drowned out the sound of the front door opening. The figure entered stealthily, approaching Booth cautiously. Their arm extended as they reached to grab Booth's shoulder. As Booth took in a deep breath, his intuition felt a presence and he whirled around in his chair. Feeling like a deer caught in headlights, he reached for his gun and slammed the tall body to the ground.

"Woah, Booth! BOOTH! Hey, it's me!" he said, raising his arms in surrender.

"Aubrey?" he blurted out, dazed.

"What, did you think I was replaced by an evil twin or something?" he replied, grinning.

"What the hell are you doing here? I thought you were going to be in Mexico for another 2 weeks."

"Well, I was – we were – but then we heard about Dr B. so we flew back immediately."

"You didn't have to do that." Booth's guilt nagged him slightly. "I've got this under control."

"I know you do, Booth." He said gently. "But when one of your best friends goes missing, leaving your best friend alone and distressed, you kinda drop everything to help in any way you can."

Booth said nothing, not being able to find the words to express his gratitude. He knew Aubrey would be a great help to him, as well as Jessica at the lab. Aubrey looked around and noticed something. "Hey, where are the mini-Booths?"

"Max took them out of D.C. I don't want them near the place with this crazy bastard around."

"Yeah that makes sense." Aubrey hesitated before continuing. "But hey if the kids are out of town, there's no way in hell you're sleeping here by yourself." Before Booth could protest, Aubrey held his hand up. "Nope. No way, Booth. If a serial killer was stalking my family, would you let me stay at home alone?"

Booth rolled his eyes, pretending to be annoyed but secretly knowing Aubrey was right.

"Whatever, fine, I'll stay at your place until we get Bones back. Why don't we go to the Hoover and I'll fill you in?"

"Sure thing."

* * *

It wasn't until 10:30pm that they parked in Aubrey's driveway, tired and frustrated at having learned nothing new of value. They both trudged inside and found Jessica at the dining room table, asleep over some x-rays.

"Hey, Jess, wake up." Aubrey whispered while giving her a gentle shove.

"Hm, what?" She sat bolt upright, startled. She sighed when she saw it was them, but her cheeks reddened as she looked at Booth. She felt embarrassed he'd caught her sleeping, she wanted him to know that she was doing everything to help him find his wife. "Sorry, I must have dozed off. I made pasta if you guys want some."

Aubrey felt slightly more alert at the mention of food. "Sure, thanks. Here Booth I'll grab you a plate, sit down."

Booth sat and placed his hands over his tense face. He was exhausted but, more than that, he was aggravated. Bones had been gone for over 12 hours now, and every minute that passed was one minute closer to her death. He missed her and the kids so much, it felt foreign to him to not be reading them a bedtime story or sharing a beer with Bones before bed. He gasped slightly, alarmed, as Aubrey placed a plate in front of him.

"You need to eat, Booth." He said. Booth merely nodded. He just wanted to go to sleep and wake up as soon as possible to get back to work.

As soon as he'd finished, he mumbled a thank you and headed to bed. Aubrey and Jessica exchanged looks of sadness for their friend's situation.

"I really miss Dr. B. The lab isn't the same without her. I can't imagine ever going to work and her not being there. I keep thinking about if anything has happened to her. What about Christine… or little Hank…" she trailed off as she began to cry.

"Hey, I know. It's okay." He said as he hugged her. "We'll find her. Booth will turn over every god damn stone in the entire country until we do. He'll never give up."

* * *

Brennan had managed to fall asleep despite the incredibly uncomfortable restraints. She was awoken by the door opening and the sound of heavy footsteps. Her eyes widened in fear as she searched around in the darkness.

"Hello, Temperance. It's nice to finally meet you."

"Who are you?"

"Oh, no one really." He laughed. "You don't know me. But I know you. I know everything about you." He smiled creepily at her. "Your favourite color is green. Your favorite song is Hot Blooded by Foreigner. Your favorite movie is Finding Nemo simply because it is your children's favorite movie. Your favorite flavour pie is cherry. But there is one thing I don't know about you that I'd like to ask." He said crouching down in front of her as his cold eyes stared into hers. His long skinny finger, lifted her chin up so that their gaze was locked.

"What is your favorite flower?"

 **A/N: I'd really appreciate a review if you have the time :) I hope you all enjoy the finale tonight! xo**


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